Hi Sven,
I've fixed the bug. Please replace
$AMBERHOME/AmberTools/src/paramfit/file_io.c with the attached file and
recompile. I will include this as part of the next bugfix for AmberTools as
well.
Let me know if you have any other problems.
Best,
Robin
On Mon, Nov 28, 2016 at 3:47 PM, Robin Betz <robin.robinbetz.com> wrote:
> Hi Sven,
>
> This is a bug in Paramfit's dihedral parameter parser. It does care about
> the order dihedrals are listed in the prmtop. As you have seen when
> conducting a multiple molecule fit where the dihedrals happen to be listed
> differently it fails to parse. I will fix this bug and send you a patch
> ASAP.
>
> You're correct that the order in which atoms are listed in a dihedral term
> shouldn't matter: A-B-C-D applies to that dihedral as well as D-C-B-A.
>
> Best,
> Robin
>
>
> On Tue, Nov 22, 2016 at 3:59 PM, Sven Hackbusch <s_hackbusch.u.pacific.edu
> > wrote:
>
>> Dear Amber Developers and Users,
>>
>> I am attempting to use paramfit from AmberTool12 to fit some dihedral
>> parameters missing from the GLYCAM forcefield.
>> I am using two small molecules (methylmethoxyacetate and methyl
>> tetrahydropyran-2-carboxylate) to fit terms for Os-Cg-C -O and Os-C
>> -Cg-Os.
>>
>> As the paramfit tutorial mentions, directionality of the dihedral terms
>> should be irrelevant (i.e. Os-Cg-C -O should be the same as O -C -Cg-Os),
>> but that does not appear to be the case:
>> When I run paramfit with the parameter file generated from one of the two
>> molecules, I get the following error in the output file:
>>
>> Reading prmtop file list: prmtops_list
>> Reading prmtop file : methylmethoxyacetate.prmtop
>> Reading prmtop file : methylTHP2carboxylate.prmtop
>> No match for dihedral O -C -Cg-Os term 0 in prmtop!
>>
>> This would indicate to me that order does matter afterall. Additionally,
>> when I generate the parameter file from the two molecules, the dihedral
>> terms are not in the same order:
>>
>> methylmethoxyacetate:
>>
>> #V2 AUTO-GENERATED PARAMETER FILE - DO NOT MODIFY
>> #
>> # BOND INFORMATION:
>> #### BOND REQ KR ####
>> #
>> # ANGLE PARAMETERS:
>> #### ANGLE KT THEQ ####
>> #
>> # DIHEDRAL PARAMETERS:
>> #### DIHEDRAL TERM KP NP PHASE ####
>> O C Cg Os 0 1 1 1
>> O C Cg Os 1 1 1 1
>> O C Cg Os 2 1 1 1
>> Os C Cg Os 0 1 1 1
>>
>> methyl tetrahydropyran-2-carboxylate:
>>
>> #V2 AUTO-GENERATED PARAMETER FILE - DO NOT MODIFY
>> #
>> # BOND INFORMATION:
>> #### BOND REQ KR ####
>> #
>> # ANGLE PARAMETERS:
>> #### ANGLE KT THEQ ####
>> #
>> # DIHEDRAL PARAMETERS:
>> #### DIHEDRAL TERM KP NP PHASE ####
>> Os Cg C Os 0 1 1 1
>> Os Cg C O 0 1 1 1
>> Os Cg C O 1 1 1 1
>> Os Cg C O 2 1 1 1
>>
>> It is not clear to me at which point the terms are defined or how to
>> change
>> their order, so I am hoping someone can point me to a solution to my
>> problem - possibly this is a mistake I made in generating the prmtop
>> files?
>>
>> Thank you very much for your help!
>>
>> -Sven
>> --
>>
>> Sven Hackbusch
>> PhD Candidate
>> Department of Chemistry
>> University of the Pacific
>>
>> <https://www.linkedin.com/pub/sven-hackbusch/53/639/aa8>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 05 2016 - 17:00:02 PST
